Design and Optimization Methods for Pin-Limited and Cyberphysical Digital Microfluidic Biochips

<p>Microfluidic biochips have now come of age, with applications to biomolecular recognition for high-throughput DNA sequencing, immunoassays, and point-of-care clinical diagnostics. In particular, digital microfluidic biochips, which use electrowetting-on-dielectric to manipulate discrete droplets (or "packets of biochemical payload") of picoliter volumes under clock control, are especially promising. The potential applications of biochips include real-time analysis for biochemical reagents, clinical diagnostics, flash chemistry, and on-chip DNA sequencing. The ease of reconfigurability and software-based control in digital microfluidics has motivated research on various aspects of automated chip design and optimization.</p><p>This thesis research is focused on facilitating advances in on-chip bioassays, enhancing the automated use of digital microfluidic biochips, and developing an "intelligent" microfluidic system that has the capability of making on-line re-synthesis while a bioassay is being executed. This thesis includes the concept of a "cyberphysical microfluidic biochip" based on the digital microfluidics hardware platform and on-chip sensing technique. In such a biochip, the control software, on-chip sensing, and the microfluidic operations are tightly coupled. The status of the droplets is dynamically monitored by on-chip sensors. If an error is detected, the control software performs dynamic re-synthesis procedure and error recovery.</p><p>In order to minimize the size and cost of the system, a hardware-assisted error-recovery method, which relies on an error dictionary for rapid error recovery, is also presented. The error-recovery procedure is controlled by a finite-state-machine implemented on a field-programmable gate array (FPGA) instead of a software running on a separate computer. Each state of the FSM represents a possible error that may occur on the biochip; for each of these errors, the corresponding sequence of error-recovery signals is stored inside the memory of the FPGA before the bioassay is conducted. When an error occurs, the FSM transitions from one state to another, and the corresponding control signals are updated. Therefore, by using inexpensive FPGA, a portable cyberphysical system can be implemented.</p><p>In addition to errors in fluid-handling operations, bioassay outcomes can also be erroneous due the uncertainty in the completion time for fluidic operations. Due to the inherent randomness of biochemical reactions, the time required to complete each step of the bioassay is a random variable. To address this issue, a new "operation-interdependence-aware" synthesis algorithm is proposed in this thesis. The start and stop time of each operation are dynamically determined based on feedback from the on-chip sensors. Unlike previous synthesis algorithms that execute bioassays based on pre-determined start and end times of each operation, the proposed method facilitates "self-adaptive" bioassays on cyberphysical microfluidic biochips.</p><p>Another design problem addressed in this thesis is the development of a layout-design algorithm that can minimize the interference between devices on a biochip. A probabilistic model for the polymerase chain reaction (PCR) has been developed; based on the model, the control software can make on-line decisions regarding the number of thermal cycles that must be performed during PCR. Therefore, PCR can be controlled more precisely using cyberphysical integration.</p><p>To reduce the fabrication cost of biochips, yet maintain application flexibility, the concept of a "general-purpose pin-limited biochip" is proposed. Using a graph model for pin-assignment, we develop the theoretical basis and a heuristic algorithm to generate optimized pin-assignment configurations. The associated scheduling algorithm for on-chip biochemistry synthesis has also been developed. Based on the theoretical framework, a complete design flow for pin-limited cyberphysical microfluidic biochips is presented.</p><p>In summary, this thesis research has led to an algorithmic infrastructure and optimization tools for cyberphysical system design and technology demonstrations. The results of this thesis research are expected to enable the hardware/software co-design of a new class of digital microfluidic biochips with tight coupling between microfluidics, sensors, and control software.</p>Dissertatio

Confocal laser scanning microscopy of nanoparticles applied to immunosorbent assays

The aim of this project was to demonstrate and develop a confocal readout method for fluorescent immunosorbent assays and investigate its potential advantages in comparison to traditional immunoassays. The key point of a confocal immunosorbent assay is the ability to detect the thin layer of immunoassay in the presence of unbound fluorescent reagents without washing the overlayer. Heterogeneous and homogeneous sandwich immunoassays of human IgG model were demonstrated successfully followed by the use of an empirical decomposition method for quantitative separation of the signals of the thin fluorescent assay layer from the overlayer. The detection limits for the homogeneous and heterogeneous formats of the model were 2.2 and 5.5 ng/ml, respectively. The application of confocal microscopy in kinetic analysis of the antigen-antibody reaction of the human IgG model was studied for homogeneous and heterogeneous formats and two fluorescent labels antibodies (FITC and QDs)

Microfluidics and Nanofluidics Handbook

The Microfluidics and Nanofluidics Handbook: Two-Volume Set comprehensively captures the cross-disciplinary breadth of the fields of micro- and nanofluidics, which encompass the biological sciences, chemistry, physics and engineering applications. To fill the knowledge gap between engineering and the basic sciences, the editors pulled together key individuals, well known in their respective areas, to author chapters that help graduate students, scientists, and practicing engineers understand the overall area of microfluidics and nanofluidics. Topics covered include Finite Volume Method for Numerical Simulation Lattice Boltzmann Method and Its Applications in Microfluidics Microparticle and Nanoparticle Manipulation Methane Solubility Enhancement in Water Confined to Nanoscale Pores Volume Two: Fabrication, Implementation, and Applications focuses on topics related to experimental and numerical methods. It also covers fabrication and applications in a variety of areas, from aerospace to biological systems. Reflecting the inherent nature of microfluidics and nanofluidics, the book includes as much interdisciplinary knowledge as possible. It provides the fundamental science background for newcomers and advanced techniques and concepts for experienced researchers and professionals

Development and evaluation of a calibration free exhaustive coulometric detection system for remote sensing.

Most quantitative analytical measurement techniques require calibration to correlate signal with the quantity of analyte. The purpose of this study was to employ exhaustive coulometry, an implementation of coulometric analysis in a stopped-flow, fixed-volume, thin-layer cell, to attain calibration-free measurements that would directly benefit intervention-free analysis systems designed for remote deployment. This technique capitalizes on the short diffusion lengths (\u3c 100 µm) to dramatically reduce the time for analysis (\u3c 30 sec). For this work, a thin-layer fluidic cell was designed in software, fabricated via CNC machining, and evaluated using Ferri/Ferrocyanide {Fe(CN)63-/4-} as a model analyte. The 2 µL fixed volume incorporated an oval, 8mm by 4 mm, thin-film gold electrode sensor with an integrated Ag|AgCl pseudo-reference electrode. The flow cell area matched the shape of the sensor, with a volume set by the thickness of a laser-cut silicone rubber gasket (~80 µm). A semi-permeable membrane isolated the working electrode and counter electrode chambers to prevent analyte diffusion. A miniaturized custom potentiostat was designed and built to measure reaction currents ranging from 10 mA to 0.1 nA. Software was developed to perform step voltammetry as well as cyclic voltammetry analysis for verifying electrode condition and optimal redox potential levels. Experimentally determined oxidation/reduction potentials of -100 mV and 400 mV, respectively, were applied to the working electrode for sample concentrations ranging from 50 µM to 10,000 µM. The current generated during the reactions was recorded and the total charge captured at each concentration was obtained by integrating the amperograms. When compared to the expected charge for a 2 µL sample, the total charge vs. concentration plots displayed a near perfect linearity over the full concentration range, and the expected charge (100 % converted) was reached within 20 seconds. The reaction currents ideally should have decayed to background levels, but exhibited constant offset values slightly larger than the background signal, a phenomenon assumed to be lingering residual flow from sample injection. After adding rigid tubing and external valves, the thin-layer cell was shown to remain within 6% of the theoretical charge after 200 seconds. Continued development of this system will offer the possibility of remote, calibration-free determinations of real-world analytes such mercury and lead

The development of microfluidic based processes

Doctor of Science (DSc) thesis.Full version unavailable due to 3rd party copyright restrictions

Solid State Circuits Technologies

The evolution of solid-state circuit technology has a long history within a relatively short period of time. This technology has lead to the modern information society that connects us and tools, a large market, and many types of products and applications. The solid-state circuit technology continuously evolves via breakthroughs and improvements every year. This book is devoted to review and present novel approaches for some of the main issues involved in this exciting and vigorous technology. The book is composed of 22 chapters, written by authors coming from 30 different institutions located in 12 different countries throughout the Americas, Asia and Europe. Thus, reflecting the wide international contribution to the book. The broad range of subjects presented in the book offers a general overview of the main issues in modern solid-state circuit technology. Furthermore, the book offers an in depth analysis on specific subjects for specialists. We believe the book is of great scientific and educational value for many readers. I am profoundly indebted to the support provided by all of those involved in the work. First and foremost I would like to acknowledge and thank the authors who worked hard and generously agreed to share their results and knowledge. Second I would like to express my gratitude to the Intech team that invited me to edit the book and give me their full support and a fruitful experience while working together to combine this book

46th Rocky Mountain Conference on Analytical Chemistry

Final program, abstracts, and information about the 46th annual meeting of the Rocky Mountain Conference on Analytical Chemistry, co-endorsed by the Colorado Section of the American Chemical Society and the Rocky Mountain Section of the Society for Applied Spectroscopy. Held in Denver, Colorado, August 1-5, 2004